Jeans, Genes, and Genomes: Cotton as a Model for Studying Polyploidy

We present an overview of the cotton genus (Gossypium) as a model for the study of polyploidy. A synopsis of the origin and evolution of polyploid cotton is provided, offering an organismal framework and phylogenetic perspective that is critical for understanding modes and mechanisms of gene and genome evolution. Sequence data from thousands of genes implicate a mid-Pleistocene (1–2 mya) origin of polyploid cotton, following trans-oceanic dispersal of an Old World, A-genome diploid to the New World and subsequent hybridization with an indigenous D-genome diploid. This chance biological reunion, occurring after 5–10 million years of diploid evolution in isolation, has led to an array of molecular genetic interactions in the newly formed allopolyploid lineage, including nonreciprocal homoeologous recombination and perhaps other forms of interlocus concerted evolution, differential rates of genomic evolution, intergenomic spread of transposable elements, and myriad forms of alterations in duplicate expression relative to that experienced in the ancestral diploids. The latter include developmental, organ-, tissue-, and cell-specific biases in homoeologous gene expression, which can be sensitive to various forms of environmental perturbation and stress. The allopolyploid Gossypium transcriptome is exceptionally dynamic, with homoeolog expression ratios being subject to change even during development of the single-celled cotton fiber. Expression evolution is temporally partitioned into changes accompanying genome merger (hybridization) at the diploid level, polyploidization, and longer term evolution at the allopolyploid level. Evidence indicates that allopolyploidy facilitated colonization of a new ecological niche for the genus and led to an enhanced capacity for developing agronomically superior cotton varieties. The myriad mechanisms that underlie genomic and regulatory evolution are suggested to have contributed to both ecological success and agronomic potential.